Many cellular events that lead to cancer and the progression of human disease represent aberrant gene expression. Our goal is to access protein-DNA interfaces in the mRNA synthesizing machinery using small molecules and gain external control of transcription pathways. This requires small molecules that can be programmed to bind with high affinity and specificity to a broad repertoire of DMA sites, permeate living human cells, traffic to the nucleus, bind DMA on chromatin and modulate transcription. Down-regulation of transcription can be envisaged to occur by disruption of transcription factor protein-DNA interfaces in promoters of genes by DMA binding small molecules or, alternatively, upregulation of transcription by recruitment of the transcriptional machinery to promoters by small molecule DNA-protein dimerizers. A core specific aim is to explore more fully inhibition of the transcription factor, hypoxia inducible factor (HIF 1a), the principal oxygen sensing molecule in vertebrates. In response to low O2, HIF 1<x controls the regulation of at least 70 genes, factors important in metabolism, angiogenesis, and cancer. We will optimize structures of DMA binding small molecules for nuclear localization;design cell permeable non-peptide molecules which combine DMA binding and activation modular domains;design artificial developmental regulators;and explore the impact of polyamide-HDAC inhibitors on chromatin. The long term goals of this program are to understand how small molecules interact with the transcriptional machinery in cells in order to externally control and reprogram gene expression. To achieve these goals, the research program combines synthetic organic chemistry, biophysical chemistry (quantitative foot printing titration, gel mobility shift assays), cell biology (confocal microscopy, qRT-PCR/mRNA, global gene expression analysis, and chromatin immunoprecipitation). Much needs to be learned about chromatin and promoter accessibility before DNA-targeted therapeutics are realized and it is our goal to contribute to this knowledge through our studies with programmable DMA binding oligomers. Our studies contribute to the basic biology of gene regulation in eukaryotic cells, and the potential of small molecule regulation of gene expression. The ability to control aberrant gene expression by cell permeable small molecules would have profound implications for human medicine.